"Methodological and force field effects in the molecular dynamics-based prediction of binding free energies of host-guest systems"

Dataset for reproducing ADFEs for host-guest systems with ORAC6.1ORAC6.1 can be downloaded form www1.chim.unifi.it/orac Directory tree .├── bin├── SP6│ ├── HREM_ions_job│ │ └── b-RSTRT│ ├── HREM_job│ │ └── b-RSTRT│ ├── lib│ ├── NE_Alchemy_ions_job│ │ └── u_ions-RSTRT│ ├── NE_Alchemy_job│ │ └── u-RSTRT│ ├── pdb│ ├── rem_start│ ├── traj│ └── work_data├── templates├── w└── WP6 ├── docking ├── HREM_job │ └── b-RSTRT ├── lib ├── NE_Alchemy_job │ └── u-RSTRT ├── pdb ├── rem_start ├── traj └── work_data SP6/WP6: contains data for WP6 host guest system see SP6[WP6]/README file for more explanations HREM_job [HREM_ions_job]: directory containing the input files for preparing and running the HREM stage NE_Alchemy_job [NE_Alchemy_ions_job]: directory for preparing and running the NE alchemical stage stage lib: contains ORAC GAFF tpgprm files pdb: contains the PDB guest and host files docking: contains the starting Vina-generated structures for the complex work_data: contains the work files for the bound and unbound NE alchemy bin: contains ancillary scripts for pre- and post-processing data traj: contain HREM-generated pdb trajectories for the bound state and apo WP6 w: contains equilibrated structure for OPC3 water templates: input templates used by scripts to produce input files for selected guest/host systems